def test_run_1():
"""Read from NumPy array file."""
# Run the algorithm.
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
run(raw_data, experiment=exp, prm=prm, probe=Probe(prb),)
# Open the data files.
with Experiment('myexperiment', dir=DIRPATH) as exp:
nspikes = len(exp.channel_groups[0].spikes)
assert exp.channel_groups[0].spikes.clusters.main.shape[0] == nspikes
assert exp.channel_groups[0].spikes.features_masks.shape[0] == nspikes
assert exp.channel_groups[0].spikes.waveforms_filtered.shape[0] == nspikes
assert isinstance(exp.channel_groups[0]._node.pca_waveforms,
tb.Array)
# Assert the log file exists.
logfile = exp.gen_filename('log')
assert os.path.exists(logfile)
assert exp.recordings[0].raw.shape == (nsamples, nchannels)
assert exp.recordings[0].high.shape == (nsamples, nchannels)
assert exp.recordings[0].low.shape[0] in range(nsamples // 16 - 2,
nsamples // 16 + 3)
assert exp.recordings[0].low.shape[1] == nchannels
def run_spikedetekt(prm_filename, dir=None, debug=False):
info = _load_files_info(prm_filename, dir=dir)
experiment_name = info['experiment_name']
prm = info['prm']
prb = info['prb']
data = info['data']
dir = dir or info['dir']
nchannels = info['nchannels']
# Make sure spikedetekt does not run if the .kwik file already exists
# (i.e. prevent running it twice on the same data)
assert not files_exist(experiment_name, dir=dir, types=['kwik']), "The .kwik file already exists, please use the --overwrite option."
# Create files.
create_files(experiment_name, dir=dir, prm=prm, prb=prb,
create_default_info=True, overwrite=False)
# Run SpikeDetekt.
with Experiment(experiment_name, dir=dir, mode='a') as exp:
# Avoid reopening the KWD file if it's already opened.
if isinstance(data, str) and data.endswith('kwd'):
data = exp._files['raw.kwd']
run(read_raw(data, nchannels=nchannels),
experiment=exp, prm=prm, probe=Probe(prb),
_debug=debug)
def run_spikedetekt(prm_filename, dir=None, debug=False):
info = _load_files_info(prm_filename, dir=dir)
experiment_name = info['experiment_name']
prm = info['prm']
prb = info['prb']
data = info['data']
dir = dir or info['dir']
nchannels = info['nchannels']
# Make sure spikedetekt does not run if the .kwik file already exists
# (i.e. prevent running it twice on the same data)
assert not files_exist(experiment_name, dir=dir, types=[
'kwik'
]), "The .kwik file already exists, please use the --overwrite option."
# Create files.
create_files(experiment_name,
dir=dir,
prm=prm,
prb=prb,
create_default_info=True,
overwrite=False)
# Run SpikeDetekt.
with Experiment(experiment_name, dir=dir, mode='a') as exp:
# Avoid reopening the KWD file if it's already opened.
if isinstance(data, str) and data.endswith('kwd'):
data = exp._files['raw.kwd']
run(read_raw(data, nchannels=nchannels),
experiment=exp,
prm=prm,
probe=Probe(prb),
_debug=debug)
def test_run_nospikes():
"""Read from NumPy array file."""
# Run the algorithm.
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
run(np.zeros((nsamples, nchannels)),
experiment=exp, prm=prm, probe=Probe(prb))
# Open the data files.
with Experiment('myexperiment', dir=DIRPATH) as exp:
assert len(exp.channel_groups[0].spikes) == 0
def test_run_canonical_pcs():
prm_canonical = prm.copy()
canonical_pcs = np.ones((prm['nfeatures_per_channel'],
prm['waveforms_nsamples'],
prm['nchannels']))
prm_canonical['canonical_pcs'] = canonical_pcs
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
run(raw_data, experiment=exp, prm=prm_canonical, probe=Probe(prb),)
def test_run_2():
"""Read from .dat file."""
path = os.path.join(DIRPATH, 'mydatfile.dat')
(raw_data * 1e4).astype(np.int16).tofile(path)
# Run the algorithm.
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
run(path, experiment=exp, prm=prm, probe=Probe(prb))
# Open the data files.
with Experiment('myexperiment', dir=DIRPATH) as exp:
assert len(exp.channel_groups[0].spikes)
def test_run_1():
"""Read from NumPy array file."""
# Run the algorithm.
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
run(raw_data, experiment=exp, prm=prm, probe=Probe(prb))
# Open the data files.
with Experiment('myexperiment', dir=DIRPATH) as exp:
print(len(exp.channel_groups[0].spikes))
# Assert the log file exists.
logfile = exp.gen_filename('log')
assert os.path.exists(logfile)
def test_diagnostics():
dir = tempfile.mkdtemp()
path = op.join(dir, 'diagnostics.py')
with open(path, 'w') as f:
f.write(
'def diagnostics(prm=None, **kwargs):\n'
' print(prm)\n'
'\n')
prm['diagnostics_path'] = path
with Experiment('myexperiment', dir=DIRPATH, mode='a') as exp:
run(np.zeros((nsamples, nchannels)),
experiment=exp, prm=prm, probe=Probe(prb))
shutil.rmtree(dir)